Mass spectrometers typically comprise a number of different ion optical elements with different modes of operation for performing different functions. Examples of the ion optical elements that a mass spectrometer may have include an element for collision induced dissociation (a collision cell), another for intermediate ion storage (such as an RF ion trap) and another for mass analysis.
Each of these different ion optical elements may be implemented using ion traps (for example, RF ion traps and/or other ion trapping devices), but each ion trap will have different pressure requirements in order to perform their different functions. For example, the mass analysis ion trap may need a very low pressure because collisions between ions and residual gas molecules may lead to scattering losses which reduce the signal intensity and sensitivity. However, the collision cell requires a high collision gas pressure, otherwise ions that enter the cell at high kinetic energies will not be trapped, since they must undergo several collisions in order to cool down sufficiently. And the ion trap used for intermediate storage may operate best at a pressure slightly below the collision cell pressure.
Each of the ion traps used for these functions may be connected to each other and gas directly supplied into the highest pressure trap such that the different gas pressures of each trap may not be treated independently from each other. For example, where the collision cell is supplied directly with gas, decreasing the pressure in the collision cell may lead to a decrease in the gas pressure in the intermediate ion storage trap, reducing the trapping efficiency therein, and a decrease in pressure in the mass analysis ion trap, increasing the signal intensity and/or resolution from the mass analysis ion trap. Therefore, the pressure of the ion traps may be a compromise between the different needs of the different ion traps in the device, for example the conflicting needs of trapping efficiency and signal intensity or resolution.
Furthermore, different types of ions may require different pressure regimes in the ion traps. For example, for bigger molecules, such as intact proteins or protein complexes, a gas pressure suitable for small molecules or bottom up proteomics may result in significantly lower sensitivity. A loss of sensitivity might make accurate analysis of results significantly more difficult, if not impossible.
Therefore, the gas pressures in the ion optical elements may also have to be a compromise to achieve the best performance for the most common uses of the mass spectrometer, such as small molecules or bottom up proteomics, at the expense of performance for less common uses.